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View Compound Workbench

The View Compound workbench

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Introduction

You can use the View Compound workbench to view, edit, and manipulate molecules. You can create a new molecule atom by atom, or you can use a molecule that has already been created.

Since both 2D and 3D representations of molecules are important in medicinal chemistry, the workbench has two workspaces, one for displaying a 2D drawing and one for displaying a 3D model. The workspaces are shown in the diagram of the workbench. You can create and edit molecules in either workspace. The workspaces are dynamically linked, so that all actions in one are reflected in the other, and the molecule is automatically updated in both workspaces. In addition, you can:

To open a View Compound workbench, click the View Compound Workbench button in the toolbar of the Stockroom (or of any open lab) or double-click a compound in the Stockroom or drag a compound and drop it onto the View Compound Workbench button.

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If the workbench was previously iconified, you can double-click its icon in the Stockroom to open the workbench.

Things you can do with the View Compound workbench

You can use the View Compound workbench to:

To change display views

The different ways of displaying molecules and hypotheses in the 2D and 3D workspaces are listed here, along with the menu item that you can use to make the changes. For example, to display a molecule with atom labels, select the View/Atom Labels menu item.

To change 3D display styles

You can display 3D molecules and hypotheses in a variety of styles, as listed here. The list also shows the menu item that you can use to achieve the effect. For example, to display a model in the wireframe style, use the Style/Wireframe menu item.

To measure interatomic values

You can measure interatomic distances, bond lengths, angles between bonds, and torsions or dihedral angles by using the Measure tool in the toolbox.

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When you select the Measure tool, it calculates all the distances and angles that it can for the number of components in the workspace that are selected. It displays all calculated values in the History Window.
For more details:

To measure distances between atoms

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Use the extend-select technique (middle mouse button) to select the atoms or bonds, then click the Measure tool. The History Window displays the distances between the first four atoms in the selection, as well as the selected angles.

You can measure the distance between bonds, atoms that are bonded together, and atoms that are not bonded together. For example, if you select A, B, and E and then select the Measure tool, the History Window displays the distances between A and B, A and E, and B and E (and also displays the angle defined by connecting A, B, and E). The value of this angle also appears in the status area.

To measure angles between bonds

Use the extend-select technique to select, in order, the three atoms that define the angle, then select the Measure tool. For example, to measure the angle formed by the bonds AB and BC, select A, B, and then C, in that order. Then click the Measure tool. The History Window displays the distances between the three atoms, and also the angle between the two bonds.

To measure torsion angles

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Use the extend-select technique to select the four atoms that define the torsion angle of interest. For example, to measure the angle between the bonds AB and DE, you should select A, then B, then D, and finally E. Then click the Measure tool.

The History Window displays the distances between all the selected atoms, the angle between each set of three atoms, and the torsion (or dihedral) angle between the AB bond and the DE bond (which is the angle formed between the ABD and BDE planes). The value of the torsion angle also appears in the status area.

For a further discussion of how to use the Measure tool see Measure tool.

To select parts of a molecule

You can select one or several bonds, atoms, and/or groups in a molecule. You also can select everything in the workspace by choosing the Edit/Select All menu item.

For more information:

Selecting atoms

If you click an atom, it becomes highlighted and selected. In the 2D workspace, a rubber band extends from the selected atom to the cursor.

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Hydrogen behaves differently: if you click a hydrogen atom in a workspace, the atom changes to the currently active element or substituent in the Periodic Table. The newly added element or substituent becomes selected and highlighted. To select a hydrogen atom without changing it, use the middle mouse button to click the hydrogen atom.

Selecting bonds

To select a bond, click it in either workspace. In the 2D and 3D workspaces, the selected bond appears highlighted. In addition, some bonds may have solid bands of highlighting, called knurls, at their ends. In the 3D workspace you can rotate a bond by dragging a knurl.

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Selecting all components that lie within a rectangular region

You can select all the atoms and bonds that lie within a rectangular area by using the mouse to draw a rectangle that encloses all the components. To do this, move the cursor to one corner of the area to be selected (not over an atom or bond) and press down the left mouse button. Keeping the left button depressed, move the cursor to the opposite corner of the area you want (but not over an atom or bond). Then release the button. All the atoms and bonds that are completely within the rectangular area become selected and highlighted. This technique is called region-selection.

Selecting all components that lie within an irregularly shaped region

Selecting a rectangular region (above) is the default type of region-selection. However, you can specify that the selection region be of any (irregular) shape. Instead of using the cursor to drag out a selection-rectangle, you can use it to draw a lasso (in this context, this means a line of any shape you want) around the components you want to select.

Use the Region-Select and Lasso-Select tools in the toolbox to specify whether you want to use the cursor to select rectangular or irregularly shaped regions, respectively:

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When lasso-select is enabled, you can draw a line around atoms you want to select. The line is drawn in blue in both the 2D and 3D graphics areas, for example:

Atoms inside the line are selected. Bonds between two atoms that are selected are selected as well:

Lasso-select works for selection of molecules, not hypotheses.

Selecting several components one at a time

Another way to select several bonds and atoms is to select the first bond or atom, and then use the middle mouse button to click each additional bond or atom to add to the selection. This technique can be used to select bonds and atoms that do not lie within a contiguous area. This technique is called extend-selection.

Deselecting selected objects

To deselect (remove the highlight from) all selected objects in the workspace, click the Deselect tool in the toolbox:

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To deselect one selected object without deselecting other selected objects, place the cursor over the object to be deselected, then click with the middle mouse button to toggle between selecting and deselecting that object without affecting the selection of other objects.

Another way to remove the highlight from all selected objects is to draw a small empty selection rectangle, thus selecting nothing (and deselecting everything else).

Window layout

To change the workbench layout

You can adjust the overall size of a workbench or the relative amounts of space dedicated to its various areas: the shelf area, the editing workspace area if there is one, and the report area if there is one. (If you want to change only the layout of the 2D and 3D workspace area, see To change the workspace layout.) The ways to change the workbench or panel size are:

To change the workspace layout

You can change the layout of the workspace. For example, you can have a large 3D workspace with a small 2D workspace in the top left corner, or you can have the 2D workspace on the left and an equal-sized 3D workspace on the right.

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To change the layout of the workspaces in your current workbench, select the Workbench/Workbench Layout menu item.

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You can choose:

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Last updated April 2000.
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